[BioC] too many biomaRt connections
sdavis2 at mail.nih.gov
Wed Apr 9 21:50:07 CEST 2008
On Wed, Apr 9, 2008 at 3:32 PM, Steffen <sdurinck at lbl.gov> wrote:
> Hi Elizabeth,
> This is an error I've recently encountered as well and has as far as I
> know nothing to do with the number of queries you performed but is a
> more general problem of the BioMart version of Ensembl.
> biomaRt is not the only tool querying this web service. Other tools
> like Taverna and custom tools using e.g. the BioMart perl API also query
> this web service.
> It looks like the BioMart system has gained popularity and recently we
> frequently hit the maximum number of connections to the MySQL database.
> Note that biomaRt doesn't query directly via MySQL but it's the MySQL
> connection at the web service that is unable to connect.
> I've contacted the Ensembl and BioMart teams and they are investigating
> this problem. It would help reporting this to helpdesk at ensembl.org to
> pressure them on this issue, showing it's not only me but many people
> who can't use their web service recently. Report this part of the error
> Too many connections at
> line 98
Just to finish the thought here, it is possible to install the MySQL
database locally and use biomaRt locally. I think this will solve the
problem for those who need regular, uninterrupted access. Steffen can
correct me if I'm wrong on this. Also, installing is not for the
faint-of-heart, as the database is pretty big.
> Elizabeth Purdom wrote:
> > Hi,
> > I am using biomaRt to get information regarding genes. I use it pretty
> > frequently and recently have gotten the error:
> > Too many connections at
> > /ebi/www/biomart/www/biomart-perl-06/lib/BioMart/Configuration/DBLocation.pm
> > line 98
> > I assume that I've hit some sort of wall in terms of how often I have
> > queried the database?
> > I don't really use biomart except through R; at what point do you get
> > booted off and what can I do to regain access? I often run queries on a
> > few hundred genes and don't think twice about rerunning such a query or
> > running several such queries in a day plus I use functions that call on
> > biomaRt repeatedly that I also apply to around 100 genes. So I could
> > easily send a thousand queries in a day. I can be more careful, but it
> > would be useful to know what the limits are. And does it matter how many
> > times you call a 'mart<-useMart(...)' command? (lately, I've been
> > calling it frequently rather than using the one I've already opened,
> > largely through programming laziness).
> > By the way, it took me quite some time to track down the error, because
> > I was using getGene which just gave me the confusing error:
> > "Error: ncol(result) == length(attributes) is not TRUE"
> > I think this must be because something like try(...) is used within
> > getBM() and so the output is the error message which is then transferred
> > down the line and at some point causes a problem when the function tries
> > to bundle it into a data.frame, etc.
> > Thanks,
> > Elizabeth
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> Steffen Durinck, PhD
> Division of Biostatistics, University of California, Berkeley &
> Life Sciences Department, Lawrence Berkeley National Laboratory
> 1 cyclotron Rd, Berkeley
> CA, 94720, USA
> Tel: +1-510-486-5202
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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